Example usage for org.springframework.batch.core JobExecution getExitStatus

List of usage examples for org.springframework.batch.core JobExecution getExitStatus

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Introduction

In this page you can find the example usage for org.springframework.batch.core JobExecution getExitStatus.

Prototype

public ExitStatus getExitStatus()

Source Link

Usage

From source file:com.javaetmoi.core.batch.test.TestParallelAndPartitioning.java

@Test
public void launchJob() throws Exception {
    // Launch the parallelAndPartitioningJob
    JobExecution execution = testUtils.launchJob();

    // Batch Status
    assertEquals(ExitStatus.COMPLETED, execution.getExitStatus());

    // Movies/*w w  w .java 2s.c  o  m*/
    assertEquals("8 movies", 8, getStepExecution(execution, "stepLogMovie").getWriteCount());

    // Music Albums
    StepExecution stepExecutionMusic = getStepExecution(execution, "stepLogMusicAlbum");
    assertEquals("11 music albums", 11, stepExecutionMusic.getWriteCount());
    Object gridSize = ExecutionContextTestUtils.getValueFromStep(stepExecutionMusic,
            "SimpleStepExecutionSplitter.GRID_SIZE");
    assertEquals("stepLogMusicAlbum divided into 2 partitions", 2L, gridSize);

    StepExecution stepExecPart0 = getStepExecution(execution, "stepLogMusicAlbumPartition:partition0");
    assertEquals("First partition processed 6 music albums", 6, stepExecPart0.getWriteCount());
    StepExecution stepExecPart1 = getStepExecution(execution, "stepLogMusicAlbumPartition:partition1");
    assertEquals("Second partition processed 5 music albums", 5, stepExecPart1.getWriteCount());
}

From source file:com.javaetmoi.elasticsearch.musicbrainz.batch.TestMusicAlbumJob.java

@Test
public void indexMusicAlbum() throws Exception {
    JobExecution execution = testUtils.launchJob();

    // Batch Status
    assertEquals(ExitStatus.COMPLETED, execution.getExitStatus());
    StepExecution indexMusicAlbum = getStepExecution(execution, "indexMusicAlbum");
    assertEquals(13, indexMusicAlbum.getWriteCount());
    assertEquals(2 * 2, indexMusicAlbum.getCommitCount());

    // Elasticsearch status
    ElasticSearchHelper.refreshIndex(client);
    DocsStatus docs = getDocStatus();//from  w  ww . ja v  a 2 s.  com
    assertEquals(13, docs.getNumDocs());
}

From source file:uk.ac.ebi.intact.editor.controller.admin.AdminJobController.java

public boolean hasJobFailed(JobExecution jobExecution) {
    return jobExecution.getExitStatus().equals(ExitStatus.FAILED);
}

From source file:org.obiba.onyx.core.service.impl.DefaultAppointmentManagementServiceImpl.java

synchronized public ExitStatus updateAppointments() {

    Map<String, JobParameter> jobParameterMap = new HashMap<String, JobParameter>();
    jobParameterMap.put("date", new JobParameter(new Date()));
    JobExecution jobExecution = jobExecutionService.launchJob(job, jobParameterMap);

    return jobExecution.getExitStatus();

}

From source file:uk.ac.ebi.eva.pipeline.jobs.steps.VepInputGeneratorStepTest.java

@Test
public void shouldGenerateVepInput() throws Exception {
    String dump = PopulationStatisticsJobTest.class.getResource("/dump/").getFile();
    JobTestUtils.restoreMongoDbFromDump(dump);
    File vepInputFile = new File(jobOptions.getVepInput());

    if (vepInputFile.exists())
        vepInputFile.delete();/*from   ww w .j a  v  a 2s  .  c  o  m*/

    Assert.assertFalse(vepInputFile.exists());

    JobExecution jobExecution = jobLauncherTestUtils
            .launchStep(VepInputGeneratorStep.FIND_VARIANTS_TO_ANNOTATE);

    Assert.assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    Assert.assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    Assert.assertTrue(vepInputFile.exists());
    TestCase.assertEquals("20\t60343\t60343\tG/A\t+", readFirstLine(vepInputFile));
    JobTestUtils.cleanDBs(VARIANTS_ANNOT_GENERATE_VEP_INPUT_DB_NAME);
}

From source file:uk.ac.ebi.eva.pipeline.jobs.steps.IndexesGeneratorStepTest.java

@Test(expected = DuplicateKeyException.class)
public void testNoDuplicatesCanBeInserted() throws Exception {
    String dbCollectionGenesName = jobOptions.getDbCollectionsFeaturesName();
    JobExecution jobExecution = jobLauncherTestUtils
            .launchStep(DatabaseInitializationJob.CREATE_DATABASE_INDEXES);

    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    MongoClient mongoClient = new MongoClient();
    DBCollection genesCollection = mongoClient.getDB(dbName).getCollection(dbCollectionGenesName);
    genesCollection.insert(new BasicDBObject("_id", "example_id"));
    genesCollection.insert(new BasicDBObject("_id", "example_id"));
}

From source file:uk.ac.ebi.eva.pipeline.jobs.steps.IndexesGeneratorStepTest.java

@Test
public void testIndexesAreCreated() throws Exception {
    String dbCollectionGenesName = jobOptions.getDbCollectionsFeaturesName();
    JobExecution jobExecution = jobLauncherTestUtils
            .launchStep(DatabaseInitializationJob.CREATE_DATABASE_INDEXES);

    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    MongoClient mongoClient = new MongoClient();
    DBCollection genesCollection = mongoClient.getDB(dbName).getCollection(dbCollectionGenesName);
    assertEquals(/*from w  w w. ja  va2  s  . com*/
            "[{ \"v\" : 1 , \"key\" : { \"_id\" : 1} , \"name\" : \"_id_\" , \"ns\" : \"" + dbName + "."
                    + dbCollectionGenesName
                    + "\"}, { \"v\" : 1 , \"key\" : { \"name\" : 1} , \"name\" : \"name_1\" , \"ns\" : \""
                    + dbName + "." + dbCollectionGenesName + "\" , \"sparse\" : true , \"background\" : true}]",
            genesCollection.getIndexInfo().toString());
}

From source file:uk.ac.ebi.eva.pipeline.jobs.AnnotationJobTest.java

@Test
public void noVariantsToAnnotateOnlyFindVariantsToAnnotateStepShouldRun() throws Exception {

    JobExecution jobExecution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    Assert.assertEquals(1, jobExecution.getStepExecutions().size());
    StepExecution findVariantsToAnnotateStep = new ArrayList<>(jobExecution.getStepExecutions()).get(0);

    assertEquals(FIND_VARIANTS_TO_ANNOTATE, findVariantsToAnnotateStep.getStepName());

    assertTrue(vepInputFile.exists());//from w  w w. j av  a2  s.  com
    assertTrue(Files.size(Paths.get(vepInputFile.toPath().toUri())) == 0);
}

From source file:uk.ac.ebi.eva.pipeline.jobs.steps.AnnotationLoaderStepTest.java

@Test
public void shouldLoadAllAnnotations() throws Exception {
    DBObjectToVariantAnnotationConverter converter = new DBObjectToVariantAnnotationConverter();

    String dump = AnnotationLoaderStepTest.class.getResource("/dump/").getFile();
    restoreMongoDbFromDump(dump);/*from   www  .  ja  v a 2 s  . co  m*/

    String vepOutput = jobOptions.getVepOutput();
    makeGzipFile(VepOutputContent.vepOutputContent, vepOutput);

    JobExecution jobExecution = jobLauncherTestUtils.launchStep(AnnotationLoaderStep.LOAD_VEP_ANNOTATION);

    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    //check that documents have the annotation
    DBCursor cursor = collection(dbName, jobOptions.getDbCollectionsVariantsName()).find();

    int cnt = 0;
    int consequenceTypeCount = 0;
    while (cursor.hasNext()) {
        cnt++;
        DBObject dbObject = (DBObject) cursor.next().get("annot");
        if (dbObject != null) {
            VariantAnnotation annot = converter.convertToDataModelType(dbObject);
            Assert.assertNotNull(annot.getConsequenceTypes());
            consequenceTypeCount += annot.getConsequenceTypes().size();
        }
    }

    assertEquals(300, cnt);
    assertTrue("Annotations not found", consequenceTypeCount > 0);
}

From source file:uk.ac.ebi.eva.pipeline.jobs.PopulationStatisticsJobTest.java

@Test
public void fullPopulationStatisticsJob() throws Exception {
    //Given a valid VCF input file
    String input = SMALL_VCF_FILE;

    pipelineOptions.put("input.vcf", input);
    variantOptions.put(VariantStorageManager.DB_NAME, STATS_DB);

    VariantSource source = new VariantSource(input, "1", "1", "studyName", VariantStudy.StudyType.COLLECTION,
            VariantSource.Aggregation.NONE);

    variantOptions.put(VARIANT_SOURCE, source);

    statsFile = new File(Paths.get(pipelineOptions.getString("output.dir.statistics"))
            .resolve(VariantStorageManager.buildFilename(source)) + ".variants.stats.json.gz");
    statsFile.delete();/*  w  ww .j  a  v a  2s. c o m*/
    assertFalse(statsFile.exists()); // ensure the stats file doesn't exist from previous executions

    initStatsLoadStepFiles();

    JobExecution jobExecution = jobLauncherTestUtils.launchJob();
    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    //and the file containing statistics should exist
    assertTrue(statsFile.exists());

    //delete created files
    statsFile.delete();
    new File(Paths.get(pipelineOptions.getString("output.dir.statistics"))
            .resolve(VariantStorageManager.buildFilename(source)) + ".source.stats.json.gz").delete();

    // The DB docs should have the field "st"
    VariantStorageManager variantStorageManager = StorageManagerFactory.getVariantStorageManager();
    VariantDBAdaptor variantDBAdaptor = variantStorageManager.getDBAdaptor(STATS_DB, null);
    VariantDBIterator iterator = variantDBAdaptor.iterator(new QueryOptions());
    assertEquals(1, iterator.next().getSourceEntries().values().iterator().next().getCohortStats().size());

    statsFileToLoad.delete();
    sourceFileToLoad.delete();
    vcfFileToLoad.delete();
}